MUTANT

Current Version

Microbial Utility Toolbox And wrapper for data traNsmission and Transformation (MUTANT) is an analysis pipeline for SARS-CoV2 that reconstructs the genome of a sequenced virus based to a reference genome and then identifies how it deviates from that reference. As part of the workflow, MUTANT incorporates Pangolin, which interprets the identified variants to assign the viral strain. Furthermore, the analysis also generates a VCF file, allowing users to examine specific mutations and view a typing summary of the isolates.

Installation

Prereq

• Install Java 8 or above (java --version)
• Install docker.
• Alternatively, install singularity:
  • On linux: conda install -c conda-forge singularity
  • On Mac/Windows follow the installation instructions here.
    • See information below on using vagrant for running singularity.

Setup

• git clone --recurse-submodules https://github.com/Clinical-Genomics/MUTANT.git
• cd MUTANT
• source setup.sh D_mutant
• source activate D_mutant
• Pull the latest image from Dockerhub or build images as described below.

Development

• Put your changes in a branch. Make a Pull Request of said branch.
• Run the self-test.
• Fill in everything you can in the PR template.
• Ping colleague and ask them to review your PR & suggest changes.
• Integrate said changes. If the changes are only aestetic, simply mention you're done without rerunning any tests.
• Merge your changes and version bump.
• Deploy new version in production.

Self-test

• source activate D_mutant
• cd MUTANT
• mutant analyse sarscov2 tests/testdata/fasta_files --profiles local,docker --config_artic mutant/config/local/default_config.json --config_mutant mutant/config/local/mutant.json --config_case tests/testdata/MIC3109_artic.json
• Wait for pipeline completion (~3m). Check results in ./results/

Or install MUTANT under S_mutant and run cg workflow mutant start frankhusky with results in /home/proj/stage/mutant/cases/frankhusky

Version bumping

MUTANTs versioning is bumped manually post PR merge, using semver standards on this variable.

Deploying new version

Deploy new version in production:

• bash mutant/standalone/deploy_hasta_update.sh production main

Docker containers

Containers are available on dockerhub. The containers can be built locally (not possible on hasta) using the instructions below.

Build docker containers

1. Start docker.
2. cd mutant/externals/gms-artic/
3. docker build -f environments/illumina/Dockerfile -t artic-ncov2019-illumina:<version> .

Push docker containers to Dockerhub

The following script will push artic-ncov2019-illumina:<version> to Dockerhub.

• docker login --username=<>
• bash mutant/standalone/push_docker_image.sh <version>

Pull containers from Dockerhub

• Automatically during analysis: Set container to clinicalgenomics/artic-ncov2019-illumina
• or pull singularity image manually: singularity pull <MUTANTDIR>/mutant/externals/gms-artic/artic-ncov2019-illumina.sif docker://clinicalgenomics/artic-ncov2019-illumina
• or pull docker image manually: docker pull clinicalgenomics/artic-ncov2019-illumina

Singularity containers

Build singularity containers

1. If needed, set up vagrant vm as below and perform Setup.
2. mutant toolbox create-images

Basics in using vagrant

• Set up the Vagrant virtual machine in an empty directory. This directory will be shared to the path /vagrant in the vm.

export VM=sylabs/singularity-ce-3.8-ubuntu-bionic64
vagrant init $VM
vagrant up
vagrant ssh

• Install conda.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b && miniconda3/bin/conda init bash && source ~/.bashrc

Basic vagrant commands:

• Configure the vm using the Vagrantfile
• Exit the vm: ctrl + d
• Destroy the vm: vagrant destroy
• Manage your boxes: vagrant box --help